Efficient simulation of stochastic chemical kinetics with the Stochastic Bulirsch-Stoer extrapolation method

BackgroundBiochemical systems with relatively low numbers of components must be simulated stochastically in order to capture their inherent noise. Although there has recently been considerable work on discrete stochastic solvers, there is still a need for numerical methods that are both fast and accurate. The Bulirsch-Stoer method is an established method for solving ordinary differential equations that possesses both of these qualities.ResultsIn this paper, we present the Stochastic Bulirsch-Stoer method, a new numerical method for simulating discrete chemical reaction systems, inspired by its deterministic counterpart. It is able to achieve an excellent efficiency due to the fact that it is based on an approach with high deterministic order, allowing for larger stepsizes and leading to fast simulations. We compare it to the Euler ?-leap, as well as two more recent ?-leap methods, on a number of example problems, and find that as well as being very accurate, our method is the most robust, in terms of efficiency, of all the methods considered in this paper. The problems it is most suited for are those with increased populations that would be too slow to simulate using Gillespie’s stochastic simulation algorithm. For such problems, it is likely to achieve higher weak order in the moments.ConclusionsThe Stochastic Bulirsch-Stoer method is a novel stochastic solver that can be used for fast and accurate simulations. Crucially, compared to other similar methods, it better retains its high accuracy when the timesteps are increased. Thus the Stochastic Bulirsch-Stoer method is both computationally efficient and robust. These are key properties for any stochastic numerical method, as they must typically run many thousands of simulations

Comparative analysis of 18S rRNA genes from Myxobolus aeglefini Auerbach, 1906 isolated from cod (Gadus morhua), Plaice (Pleuronectes platessa) and dab (Limanda limanda), using PCR-RFLP

The myxosporean parasite Myxobolus aeglefini is a marine species, which can be found in the cartilage of mainly gadid fish species. The parasite has, however, been recorded in the flatfish plaice (Pleuronectes platessa) and dab (Limanda limanda). It is not clear if isolates from unrelated hosts represent the same species. Therefore a molecular study was conducted to reveal differences at the DNA level between these isolates. PCR was successfully conducted on three different isolates of Myxobolus aeglefini sampled from cod (Gadus morhua), plaice and dab respectively, using 18S rDNA as template. A PCR product of approx. 1600 base pairs was obtained and RFLP (Restriction Fragment Length Polymerase) was conducted on the fragment with the restriction enzymes Hinf I, Msp I and Hae III. No differences between the isolates were found, suggesting that the three isolates represent the same species

Higher-order numerical methods for stochastic simulation of\ud chemical reaction systems

In this paper, using the framework of extrapolation, we present an approach for obtaining higher-order -leap methods for the Monte Carlo simulation of stochastic chemical kinetics. Specifically, Richardson extrapolation is applied to the expectations of functionals obtained by a fixed-step -leap algorithm. We prove that this procedure gives rise to second-order approximations for the first two moments obtained by the chemical master equation for zeroth- and first-order chemical systems. Numerical simulations verify that this is also the case for higher-order chemical systems of biological importance. This approach, as in the case of ordinary and stochastic differential equations, can be repeated to obtain even higher-order approximations. We illustrate the results of a second extrapolation on two systems. The biggest barrier for observing higher-order convergence is the Monte Carlo error; we discuss different strategies for reducing it

Risks perceptions and risk management instruments in the European Union: Do farmers have a clear idea of what they need?

This paper explores and analyzes farmers’ risk perceptions, risk management instruments’ demand and usage in five Member States (Hungary, Spain, the Netherlands, Germany and Poland). A survey completed by 1047 representative farmers of these EU Member Status collected information that allowed us to set apart two focus areas: the first looks at the declared importance of several sources of farms’ risk and income instability, and at the actual means that farmers pursue to manage and face them. The second area focuses on the demand for risk management instruments. The paper’s objective is to determine the factors that explain farmers’ responses in the first area, and based on those factors, analyse the demands for two instruments (insurance, and future & option markets). After carrying out basic descriptive statistic analyses, we perform factor analysis in order to establish the linkages between the perceptions and ranking of risks with the declared strategies to manage them. Logit models were fit to determine potential demand of insurance, and futures & options based on the three factors, and other variables like activity types and other controls, like nationality. Results from the factor analysis show that the perception of risk and actual use of risk management are very diverse. Logit models show that insurance is clearly an alternative instrument to diversification, but its demand is poorly explained by the other factors. Furthermore the demand for the use of futures and options is explained by the three factors, with the volatility factor, positively linked; market access /contractual risks; and diversification, negatively linked. In conclusion, policy makers should proceed with caution selecting the most adequate risk management instruments for farmers. It appears that the expected demand of risk management tools does not fit perfectly with the stated perception of risks

Analogies between the crossing number and the tangle crossing number

Tanglegrams are special graphs that consist of a pair of rooted binary trees with the same number of leaves, and a perfect matching between the two leaf-sets. These objects are of use in phylogenetics and are represented with straightline drawings where the leaves of the two plane binary trees are on two parallel lines and only the matching edges can cross. The tangle crossing number of a tanglegram is the minimum crossing number over all such drawings and is related to biologically relevant quantities, such as the number of times a parasite switched hosts. Our main results for tanglegrams which parallel known theorems for crossing numbers are as follows. The removal of a single matching edge in a tanglegram with $n$ leaves decreases the tangle crossing number by at most $n-3$, and this is sharp. Additionally, if $\gamma(n)$ is the maximum tangle crossing number of a tanglegram with $n$ leaves, we prove $\frac{1}{2}\binom{n}{2}(1-o(1))\le\gamma(n)<\frac{1}{2}\binom{n}{2}$. Further, we provide an algorithm for computing non-trivial lower bounds on the tangle crossing number in $O(n^4)$ time. This lower bound may be tight, even for tanglegrams with tangle crossing number $\Theta(n^2)$.Comment: 13 pages, 6 figure

Observation of a local gravity potential isosurface by airborne lidar of Lake Balaton, Hungary

Airborne lidar is a remote sensing method commonly used for mapping surface topography in high resolution. A water surface in hydrostatic equilibrium theoretically represents a gravity potential isosurface. Here we compare lidar-based ellipsoidal water surface height measurements all around the shore of a major lake with a local high-resolution quasi-geoid model. The ellipsoidal heights of the 87 km2 we sampled all around the shore of the 597 km2 lake surface vary by 0.8m and strong spatial correlation with the quasi-geoid undulation was calculated (R2 = 0.91). After subtraction of the local geoid undulation from the measured ellipsoidal water surface heights, their variation was considerably reduced. Based on a network of water gauge measurements, dynamic water surface heights were also successfully corrected for. This demonstrates that the water surface heights of the lake were truly determined by the local gravity potential.We conclude that both the level of hydrostatic equilibrium of the lake and the accuracy of airborne lidar were sufficient for identifying the spatial variations of gravity potential

Developing social capital in implementing a complex intervention: a process evaluation of the early implementation of a suicide prevention intervention in four European countries

&lt;p&gt;Background: Variation in the implementation of complex multilevel interventions can impact on their delivery and outcomes. Few suicide prevention interventions, especially multilevel interventions, have included evaluation of both the process of implementation as well as outcomes. Such evaluation is essential for the replication of interventions, for interpreting and understanding outcomes, and for improving implementation science. This paper reports on a process evaluation of the early implementation stage of an optimised suicide prevention programme (OSPI-Europe) implemented in four European countries.&lt;/p&gt; &lt;p&gt;Methods: The process analysis was conducted within the framework of a realist evaluation methodology, and involved case studies of the process of implementation in four European countries. Datasets include: repeated questionnaires to track progress of implementation including delivery of individual activities and their intensity; serial interviews and focus groups with stakeholder groups; and detailed observations at OSPI implementation team meetings.&lt;/p&gt; &lt;p&gt;Results: Analysis of local contexts in each of the four countries revealed that the advisory group was a key mechanism that had a substantial impact on the ease of implementation of OSPI interventions, particularly on their ability to recruit to training interventions. However, simply recruiting representatives of key organisations into an advisory group is not sufficient to achieve impact on the delivery of interventions. In order to maximise the potential of high level ‘gatekeepers’, it is necessary to first transform them into OSPI stakeholders. Motivations for OSPI participation as a stakeholder included: personal affinity with the shared goals and target groups within OSPI; the complementary and participatory nature of OSPI that adds value to pre-existing suicide prevention initiatives; and reciprocal reward for participants through access to the extended network capacity that organisations could accrue for themselves and their organisations from participation in OSPI.&lt;/p&gt; &lt;p&gt;Conclusions: Exploring the role of advisory groups and the meaning of participation for these participants revealed some key areas for best practice in implementation: careful planning of the composition of the advisory group to access target groups; the importance of establishing common goals; the importance of acknowledging and complementing existing experience and activity; and facilitating an equivalence of benefit from network participation.&lt;/p&gt

The influence of a hot environment on parental cooperation of a ground-nesting shorebird, the Kentish plover Charadrius alexandrinus

<p>Abstract</p> <p>Background</p> <p>Parental care often increases offspring survival, but is costly to the parents. A trade-off between the cost and benefit of care is expected, so that when care provisioning by both parents is essential for the success of young, for instance in extremely cold or hot environments, the parents should rear their young together. We investigated the latter hypothesis in a ground nesting shorebird, the Kentish plover <it>Charadrius alexandrinus </it>in an extremely hot environment, the Arabian Desert. Midday ground temperature was often above 50°C in our study site in Abu Dhabi (United Arab Emirates), thus leaving the eggs unattended even for a few minute risks overheating and death of embryos.</p> <p>Results</p> <p>Through the use of video surveillance systems we recorded incubation routines of male and female Kentish plovers at 28 nests over a full day (24 h). We show that ambient temperature had a significant influence on incubation behaviour of both sexes, and the relationships are often non-linear. Coordinated incubation between parents was particularly strong in midday with incubation shared approximately equally between the male and the female. The enhanced biparental incubation was due to males increasing their nest attendance with ambient temperature.</p> <p>Conclusions</p> <p>Our results suggest biparental care is essential during incubation in the Kentish plover in extremely hot environments. Shared incubation may also help the parents to cope with heat stress themselves: they can relieve each other frequently from incubation duties. We suggest that once the eggs have hatched the risks associated with hot temperature are reduced: the chicks become mobile, and they gradually develop thermoregulation. When biparental care of young is no longer essential one parent may desert the family. The relaxed demand of the offspring may contribute to the diverse breeding systems exhibited by many shorebirds.</p

A logic road from special relativity to general relativity

We present a streamlined axiom system of special relativity in first-order logic. From this axiom system we "derive" an axiom system of general relativity in two natural steps. We will also see how the axioms of special relativity transform into those of general relativity. This way we hope to make general relativity more accessible for the non-specialist

Observations on non-randomly distribution of spores of Henneguya spp. (Cnidaria, Myxosporea, Myxobolidae) within plasmodia

Species of the cnidarian genus Henneguya Thelohan, 1892 (Myxosporea: Myxobolidae) are histozoic parasites commonly found in freshwater and, more rarely, in marine fish. The development of these parasites in fish tissues includes the formation of plasmodia within which occurs the sporogony originating spores with two caudal processes, which are usually randomly distributed within the plasmodia. In this report the authors present some cases of non-random distribution of the spores of six species of Henneguya within their plasmodia. Two different patterns of non-random distribution were found based on a literature survey. These patterns and their origin are discussed. Apparently this non-random distribution of the spores is due to both internal and external factors.European Regional Development Fund (ERDF) through the COMPETE - Operational Competitiveness Programmenational funds through FCT - Foundation for Science and TechnologyCNPqGINOPUniv Porto, Fac Ciencias, Dept Biol, Rua Campo Alegre,Edificio FC4, P-4169007 Oporto, PortugalCIMAR, CIIMAR, Ctr Interdisciplinar Invest Marinha & Ambiental, Matosinhos, PortugalInst Super Engn Porto, Lab Engn Matemat LEMA, Oporto, Portugal|Univ Fed Sao Paulo, UNIFESP, Dept Ecol & Biol Evolut, Diadema, SP, BrazilUniv Estadual Campinas, Inst Biol, Dept Biol Anim, Campinas, SP, BrazilCtr Agr Res, Inst Vet Med Res, Budapest, HungaryHungarian Acad Sci MTA, Budapest, HungaryUniv Fed Sao Paulo, UNIFESP, Dept Ecol & Biol Evolut, Diadema, SP, BrazilEuropean Regional Development Fund (ERDF) through the COMPETE - Operational Competitiveness Programmenational funds through FCT - Foundation for Science and Technology: PEst-C/MAR/LA0015/2013CNPq: 305630/2013-0GINOP: 2.3.3-15-2016-00004Web of Scienc